Diagnostic genomic analysis is prognostic in AYA patients with ALL treated on an MRD-stratified pediatric protocol

Next-generation sequencing has enabled classification of multiple new recurrent genomic drivers of acute lymphoblastic leukemia (ALL). We aimed to describe the genomic drivers of ALL in an adolescent and young adult (AYA) cohort (ALL06; target age, 15-39 years; recruited age, 16.6-39 years), treated uniformly on a pediatric-inspired protocol (the Australasian Leukaemia and Lymphoma Group ALL06 study). ALL06 assessed the safety and efficacy of adapting a pediatric chemotherapy protocol in older patients. Genomic risk classification of enrolled B-ALL and T-ALL patients was based on multiple assays: messenger RNA sequencing, multiplex ligation-dependent probe amplification, immunophenotyping, and cytogenetics. Using this approach, 36 of 40 (90%) patients with B-ALL and 13 of 17 (76.5%) patients with T-ALL were classified according to genomic risk. A strong correlation existed between adverse genomic risk and minimal residual disease (MRD) at the end of consolidation, translating to inferior overall and relapse free survival. Patients with adverse risk genomics who achieved negative MRD status had improved responses compared with those with persistent MRD. Patients with standard-risk genomics had excellent responses regardless of MRD status. This is the first report of the impact of genomics in an individual cohort of AYA patients treated on a single protocol. These data argue strongly for incorporation of a genomic risk classification into future ALL treatment paradigms at the time of diagnosis, and also for the rigorous assessment of risk assignments in a group of patients who are not children and not older adults. This trial was registered at https://anzctr.org.au/ as #ACTRN12611000814976.